Admin: Pierre Lindenbaum

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Posts by Pierre Lindenbaum

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Comment: C: Identifying Gene name
... it's kamoulox ...
written 22 hours ago by Pierre Lindenbaum99k
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Comment: C: Explain fig. 5 c of "The impact of rare variation on gene expression across tiss
... @aditi.qamra @cpad0112 thanks for the colored-dots ! :-) I still don't get the whole figure itself. How should I read it ? Why is it interesting ? ...
written 23 hours ago by Pierre Lindenbaum99k
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Comment: C: Identifying Gene name
... it's not clear, from which file do you need to get the gene name ? why do you cite the BAM ? why do you search the "sequence" ? ...
written 1 day ago by Pierre Lindenbaum99k
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Explain fig. 5 c of "The impact of rare variation on gene expression across tissues" doi:10.1038/nature24267
... In > "The impact of rare variation on gene expression across tissues" Nature 550, 239–243 (12 October 2017) doi:10.1038/nature24267 As far as I understand, using the GTex data, the authors have written a predictive algorithm (RIVER) to predict the consequences on gene expression of a se ...
variant article expression paper rare written 1 day ago by Pierre Lindenbaum99k • updated 22 hours ago by aditi.qamra230
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Comment: C: samtools tview type consensus sequence to stdout
... this is not my cmd-line: I redefine/override COLUMNS each time I run samtools: $ COLUMNS=1000 samtools tview -d ... ...
written 1 day ago by Pierre Lindenbaum99k
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Comment: C: GATK filtering console error
... you're using `-T SelectVariants` (https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_variantutils_SelectVariants.php) while **--filterExpression** is an option for **VariantFiltration** https://software.broadinstitute.org/gatk/documentatio ...
written 3 days ago by Pierre Lindenbaum99k
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Comment: C: GATK filtering console error
... ok, I've looked at the syntax of srun: https://www.dkrz.de/up/doku/mistral/running-jobs/using-srun as far as I can see , you have to put GenomeAnalysisTK -T SelectVariants -R reference.fa -V raw_variants.vcf --filterExpression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 ...
written 3 days ago by Pierre Lindenbaum99k
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Answer: A: GATK filtering console error
... **quote** the expression: srun 'GenomeAnalysisTK -T SelectVariants -R reference.fa -V raw_variants.vcf --filterExpression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0" --filterName "my_snp_filter" -o filtered_variants.vcf' ...
written 3 days ago by Pierre Lindenbaum99k
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Answer: A: samtools tview type consensus sequence to stdout
... > I know samtools tview has a -d T option, but it only outputs 80 columns or so. you can override the `${COLUMNS}` shell's variable. $ COLUMNS=1000 samtools tview -d T in.bam but beware for the memory required to print a large matrix. ...
written 4 days ago by Pierre Lindenbaum99k
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Answer: A: Copy Sample ID from VCF file to ID column
... assuming your VCF is **really** a VCF file and using bioalcidae http://lindenb.github.io/jvarkit/BioAlcidaeJdk.html java -jar dist/bioalcidaejdk.jar -e 'println("ID\t"+header.getSampleNamesInOrder().stream().collect(Collectors.joining("\t")));stream().filter(V->V.hasID()).forEach(V->pri ...
written 4 days ago by Pierre Lindenbaum99k

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Scholar 3 days ago, created an answer that has been accepted. For A: conditional replacing rows with 9
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: Annotate A Vcf File
Scholar 3 days ago, created an answer that has been accepted. For A: conditional replacing rows with 9
Scholar 4 days ago, created an answer that has been accepted. For A: conditional replacing rows with 9
Appreciated 4 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Scholar 4 days ago, created an answer that has been accepted. For A: conditional replacing rows with 9
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: Annotate A Vcf File
Appreciated 6 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
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Scholar 12 days ago, created an answer that has been accepted. For A: conditional replacing rows with 9
Scholar 12 days ago, created an answer that has been accepted. For A: conditional replacing rows with 9
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Scholar 20 days ago, created an answer that has been accepted. For A: removing decimal from ENSEMBLE gene ID from deseq2 output
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Scholar 21 days ago, created an answer that has been accepted. For A: removing decimal from ENSEMBLE gene ID from deseq2 output

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